ACR ISP mkII

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Hi,
I am new to AVR, and in general my knowledge of electronics is pretty limited. I just got an STK500, Atmega644, and since I don't have a COM port on my laptop I bought an AVR ISP mkII. Since I have gotten the parts I spent a good 4 hours sitting and looking at flashing LED's. I can't get AVR studio to locate the board, let alone program anything. I was wondering if somebody can give me some pointers regarding the correct jumper settings for the mkII and/or links to an appropriate website document. Everything I came across so far assumes a good level of familiarity with hardware, which I really don't have at this point. Help, please?

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This thread is addressing the very same problem with the AVRISP MKII:
https://www.avrfreaks.net/index.php?name=PNphpBB2&file=viewtopic&t=59066

IDE - Eclipse w/AVR Eclipse plugin
Programmer - AVRISP MKII
OS - Ubuntu (Intrepid) Linux